https://techcommunity.microsoft.com/t5/outlook-global-customer-service/how-outlook-2016-utilizes-exchange-server-2016-fast-search/ba-p/381195#

Secondary mailboxes

When Outlook 2016 released, the plan was to only support FAST search on your primary mailbox. However, starting in the Fall of 2017, you should see that any Exchange email account added through File | Account Settings (also known as MultiEx or multiple Exchange accounts) now fully supports FAST search.

If you are limited to using an older build of Outlook 2016 and search in a MultiEx mailbox, the FAST query may be submitted in the context of the logged on user (you). This causes the search results to be pulled from your own mailbox, not the secondary mailbox that currently has the focus in your Outlook client. If you are unable to upgrade your Outlook 2016 client to the November 2017 Monthly Channel Build, you can temporarily work around this limitation by using one of the following options:

• Change the search scope to All Outlook Items, Subfolders, or All Mailboxes
• Disable Outlook 2016’s use of FAST search via policy or local user registry setting (see the next section)

Note Other types of secondary stores, such as those added via Open these additional mailboxes or those that are automatically configured via AutoMapping, are still limited to WDS.

HOWEVER

I’ve found users report searching still sucks in their shared and/or secconday mbxs. So per document set the below DWORD key to 1 if a user reports this – though I’m still waiting to hear if there are negative connotations to this change